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Based on the final episode of Season 6 of Game of Thrones, we learn that Jon is not the bastard child of Ned Stark but rather his nephew.

Seeing as Lyanna was taken by the Targaryen's, does that mean that his father was Rhaegar? Making him the nephew of Daenerys?

If this is the case, who between the two of them, has a stronger claim on the throne?

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That's a difficult one...

Assuming that GoT uses something similar to the British rules of ascension(See Note), then Jon would have the rightful claim...

Succession to the British throne is determined by descent, gender, legitimacy, and religion. Under common law, the crown is inherited by an individual's children and by a childless individual's nearest collateral line.

...except that he would still not be a legitimate heir, as he would be the bastard son of Rhaegar & Lyanna, rather than Elia.

On the other hand, Daenerys would nominally be eligible even if Jon was legitimate but only if GoT were using rules changed after the release of A Dance with Dragons.
British succession now [since 2015] casts all children in descending order by date of birth [absolute primogeniture], no longer just the male line [male-preference primogeniture] . The law is not retrograde, which means that, for instance, Anne is not suddenly promoted to 2nd in line after Charles.

However - it is unlikely that GoT, the series or the books, will be using that system in its modern state. It is far likely to be using the earlier medieval system from which it derived...

The current succession law in the United Kingdom evolved from succession law in both England and Scotland. Originally in both countries, there were no fixed rules governing succession to the throne. The individual could have relied on inheritance, statute, election (by Parliament or by another body), nomination (by a reigning sovereign in his or her will), conquest or prescription (de facto possession of the Crown). It was often unclear which of these bases should take precedence; often, the outcome depended not on the legal strength of the claims, but on the political or military power of the claimants.

However, over time, the default rule became male primogeniture: later monarchs coming to the throne by exception to this rule went to great lengths to explain and justify going against these rules, and to prove their rivals illegitimate. Eventually, Parliament took control of succession.

Westeros/The Seven Kingdoms has no parliament, so it seems we are back to it being the one with the strongest army.

There is, however, one more potential spanner in the works [spoilers from the books]

Though he has yet to put in any appearance in the TV shows, in the books we have already seen the return of Jon Connington [hand of the king to Aerys II] along with a character (Young Griff) believed to actually be Aegon Targaryen, the surviving son of Rhaegar.

If proven, then he would be the legitimate heir, by the medieval male-preference primogeniture rules.

Note Reasoning for that assumption is because everything else in the series seems roughly modelled on medieval Britain, even down to the regional placement of the actor's accents, except for 'Scotland' North of the Wall, for which they have been using Scandinavian accents, presumably to not offend the Scots, & Dorne [Cornwall] which is the only one of the seven Kingdoms that doesn't appear 'British' at all.

Update after comments.
It would appear that the Targaryens have, since the Dance of the Dragons (129 -131 AC) used a method of agnatic primogeniture rather than male-preference.

From awoiaf: Targaryens
Since the Dance, House Targaryen has practiced a highly modified version of agnatic primogeniture, placing female claimants in the line of succession behind all possible male ones, even collateral relations.

Though that would still only [if at all, in an agnatic system] place Daenerys behind Jon in succession order if Jon's legitimacy was proven.

As we currently have a queen on the throne, as of S06E10, then I think we could say there is precedence for Daenerys' claim.

I still think it will come down to who has the most powerful army - though we know the plot will never be that simple, but it's out of scope to start wondering whether they'll join forces to fight the Night King.

One further point to ponder - and to which I don't know the answer as I'm no expert on agnatic primogeniture
...would Daenerys' marriage to Hizdahr zo Loraq give him precedence over her?

Sources:
Wikipedia:
Succession to the British throne
A Wiki of Ice & Fire:
Rhaegar Targaryen
Lyanna Stark

  • I think TV show is completely skipping him and lady stoneheart – Ankit Sharma Jun 28 '16 at 7:06
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    Why do you base your answer on the British rules, rather than the books, where the rules of succession are described? – Chanandler Bong Jun 28 '16 at 8:16
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    I think the geography and accents are based on the Viking age in England (later 8th c. thru mid 11th c.). Where the heathen enemies of the north would have been Scandinavian. The northern half of England is loaded with Norse place names. Whereas the southern part is dominated by Saxon names – Tom Jun 28 '16 at 18:02
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    @Tom - I'd never have placed Dornish accents as 'french' - 'vague european with hints of old eastern block mixed with iffy spanish' would be as close as I've got ;-) I just watched the bit from S06E01 & I'd have to add 'dodgy kebab shop turkish-ish' to that definition. No french in sight. [reposted to fix confusing typo] – disassociated Jun 28 '16 at 18:15
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    FYI, HBO has confirmed that Rhaegar is the father: makinggameofthrones.com/production-diary/… – Ivo Beckers Jun 29 '16 at 22:44
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No, Jon has no claim to the Iron Throne. The Targaryens have lost the throne to the Baratheons, and Robert become king by "Right of Conquest" and now Daenerys is going to take it with the same.

So it is not an old line of sucession. This is a new line starting from Daenerys, as Jon can claim the throne after Daenerys by succession.

However, that does have many technical issues: it is the audience/fans who know that Jon is Targ. However, within canon, he is just Ned's bastard, now King in the North. In the same way, Stannis was denied his throne.

Currently Cersei is the rightful queen by right of conquest, as she is styling herself Cersei Lannister.

  • She is mother of last king as per public knowledge. And she is wife of last king Robert. If bastardy of her children known , she has right before them but after Stannis & Renly. – Panther Jun 28 '16 at 10:31
  • She killed the existing queen and lots of other members of council, i don't think rest (if any) will be in any agreement with her. So it is more of conquest – Ankit Sharma Jun 28 '16 at 10:33
  • If you look at Robert's Rebellion, while in actuality he took the throne through conquest, even he used the right of succession (being a distant cousin to the Targaryens) to justify his rule. And Daenerys is claiming the throne as the daughter of the overthrown king (see the Targaryens refer to Robert as the "Usurper") in the books. So questions about succession are legitimate. – kuhl Jun 28 '16 at 14:23
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    The fact that Jon Snow is King in the North is itself indicative of succession laws. Jon Snow is a bastard, who had no rights as a bastard but even less so after joining the Night's Watch, and was STILL hailed as King in the North while a legitimate female successor to House Stark was present - Sansa Stark, daughter of Ned Stark, sister to the last King in the North, and wife of Ramsay Bolton the last Lord of Winterfell, was sitting next to him. – DariM Jun 29 '16 at 0:29
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The show implied

Rhaegar to be Jon's father, but HBO later confirmed in an infographic that it was true.

However, a lot of people still forget that there is no record of Rhaegar marrying Lyanna. According to the stories, she was abducted by him. This would make Jon Snow a bastard. But he already is known to be one! Just that he would now be called Jon Waters instead of Snow as Waters is the bastard name given to people from King's Landing and Dragonstone.

As for his claim on the throne, being a bastard he has not direct claim. Only if the king's (Aerys II) blood line was completely destroyed, could a bastard of the family take power. He would be required to use inverted colors in his sigil though.

So if you ignore Robert's rebellion and are in for the Targaryens, then Dany is the rightful heir. However by the right of conquest, Robert held the throne and only his descendants are now the rightful heirs. Does not looks like that matters now though.

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Q: Does that mean that his father was Rhaegar? Making him the nephew of Daenerys?

A: It is so strongly implied that it can pretty much be taken as truth.

Regarding your question on his potential claim, he certainly would be in line, but there are many factors. Tetsujin & al'thor's answer is quite comprehensive.

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